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Table 3: Example of consensus prediction for the protein 7rsa obtained by weighted average. In the table a small part of the HSSP alignment is shown for only 3 out of a total of 56 proteins in the alignment. For each protein is shown the predictions of (left to right) -helix, -strand and coil produced by the ensemble method. Note that a \* quot; in the amino acid sequence corresponds to a gap in the alignment. The column \Weighted average quot; is the weighted average consensus prediction for each of the three secondary structures. The two last columns show the predicted and observed structures respectively.

in Improving Prediction of Protein Secondary Structure using Structured Neural Networks and Multiple Sequence Alignments
by Søren Kamaric Riis, Anders Krogh 1996
Cited by 48

Table 9: List of the start position and the sequence homology of detected conserved RNA structures of selected groups. The consensus panhandle structure of all sequences is shown in gure 33. In group 2 and 3 additional RNA secondary structures are found. Conserved RNA motifs labeled (*) are commonly predicted in group 2, 3 and also in sense and anti-sense RNA, see gure 37.

in der Universität Wien von
by Mag Martin Fekete, Molekulare Strukturbiologie, Meinen Eltern, Geniale Gedanken, Tolle Sprüche, Zuerst Zeit Für

Table 4. Accuracy of PsiCSI, CSI, and Psipred on the regions with well-defined secondary structure

in Accurate and Automated Classification of
by Protein Secondary Structure
"... In PAGE 4: ... Thus, the training set was further restricted to residues in which the level of agreement on secondary structure was at least 90%, which accounted for a large majority (85%) of the residues. The accuracies of the different methods over this subset of residues and over the entire set of residues are shown in Table4 . Table 5 lists all of the proteins in the test set and the Q3 accuracies using PsiCSI, CSI, and Psipred.... ..."

Table 2: Abbreviations of secondary structures.

in Protein structure prediction based on secondary structure alignment
by Rei-sing Cheng, Chang-biau Yang, Kuo-tsung Tseng 2004
"... In PAGE 3: ...The secondary structure expression we use here is according to an implementation of the method pro- posed by Kabsch and Sander [14]. Table2 shows the abbreviation of each secondary structure. 3 A Novel Sequence Alignment Algo- rithm with Protein Secondary Struc- ture in Consideration In this section, we shall propose a new protein alignment algorithm, which considers the combined information of primary structures and secondary struc- tures.... ..."
Cited by 1

Table 4. Performance of the three other servers (PSI-PRED, PROF-SEC, PHD) and our three feature sets on the EVA150 database with respect to different secondary structure prediction quality measurements.

in A new representation for protein secondary structure prediction based on frequent patterns
by Fabian Birzele , Stefan Kramer
"... In PAGE 6: ... In Table 5 the results of consensus pre- dictions without and with FPPS can be found. The performance of the individual methods can be found in Table4 . It is important to note that the results of individual methods and those of consensus methods cannot be compared easily, because consensus results are based on AODE predictions from 10-fold cross-validation, whereas individual results are obtained directly as outputs from the predic- tion methods compared here.... ..."

Table 4. Performance of the three other servers (PSI-PRED, PROF-SEC and PHD) and our three feature sets on the EVA150 database with respect to different secondary structure prediction quality measurements

in A new representation for protein secondary structure prediction based on frequent patterns
by Fabian Birzele, Stefan Kramer
"... In PAGE 6: ... In Table 5 the results of consensus predictions without and with FPPS can be found. The performance of the individual methods can be found in Table4 . It is important to note that the results of individual methods and those of consensus methods cannot be compared easily, because consensus results are based on AODE predictions from 10-fold cross-validation, whereas individual results are obtained directly as outputs from the predic- tion methods compared here.... ..."

Table 2. Corresponding regions of the secondary and super- secondary structure constraints.

in A multi-objective evolutionary approach to the protein structure prediction problem
by Vincenzo Cutello 2006
Cited by 2

Table 1. Folding Algorithms for RNA Secondary Structures.

in Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration - I. Neutral Networks
by Walter Grüner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
"... In PAGE 5: ... A variety of computer programs predicting RNA secondary structures have been published. A very brief overview is given in Table1 . Two public domain packages for RNA folding are currently available by anonymous ftp: Zuker apos;s mfold [25] and the Vienna RNA Package [26].... ..."

Table 1. Folding Algorithms for RNA Secondary Structures.

in Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
by Walter Grüner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
"... In PAGE 6: ...: Analysis of RNA Sequence-Structure Maps A variety of computer programs predicting RNA secondary structures have been published. A very brief overview is given in Table1 . Two public domain packages for RNA folding are currently available by anonymous ftp: Zuker apos;s mfold [24] and the Vienna RNA Package [25].... ..."

Table 1. Predicted Secondary Structure Elements.

in Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
by Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, Peter F. Stadler
"... In PAGE 15: ...As a second example we have re-analyzed a sample of HIV1 sequences from an earlier study [17]. The number of predicted conserved base pairs is similar to the Hepatitis C case, see Table1 for details. In the following we discuss the automatically generated predictions for two well-understood secondary structure motifs, namely TAR and RRE, in some detail.... ..."
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